Epigenomics and transcriptomics profiles of developing zebrafish heart cells

Gulrez Chahal; Michael P. Eichenlaub; Markus Tondl; Michał Pawlak; Monika Mohenska; Lin Grimm; Lauren Bottrell; Mark Drvodelic; Sara Alaei; Jeannette Hallab; Lisa N. Waylen; Jose M. Polo; Cédric Blanpain; Nathan Palpant; Fernando J. Rossello; Minna Liisa Änkö; Peter D. Currie; Benjamin M. Hogan; Cecilia Winata; Ekaterina Salimova; Hieu T. Nim; Mirana Ramialison

doi:10.1038/s41597-025-05895-9

Epigenomics and transcriptomics profiles of developing zebrafish heart cells

Gulrez Chahal
, Michael P. Eichenlaub
, Markus Tondl
, Michał Pawlak
, Monika Mohenska
, Lin Grimm
, Lauren Bottrell
, Mark Drvodelic
, Sara Alaei
, Jeannette Hallab
, Lisa N. Waylen
, Jose M. Polo
, Cédric Blanpain
, Nathan Palpant
, Fernando J. Rossello
, Minna Liisa Änkö
, Peter D. Currie
, Benjamin M. Hogan
, Cecilia Winata
, Ekaterina Salimova

Hieu T. Nim^*, Mirana Ramialison^*

^*Corresponding author for this work

Biosciences

Research output: Contribution to journal › Data article › peer-review

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Abstract

cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.

Original language	English
Article number	1620
Number of pages	10
Journal	Scientific Data
Volume	12
DOIs	https://doi.org/10.1038/s41597-025-05895-9
Publication status	Published - 2025
Publication type	A1 Journal article-refereed

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Publication forum classification

Publication forum level 1

ASJC Scopus subject areas

Statistics and Probability
Information Systems
Education
Computer Science Applications
Statistics, Probability and Uncertainty
Library and Information Sciences

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10.1038/s41597-025-05895-9Licence: CC BY

Epigenomics and transcriptomics profiles of developing zebrafish heart cellsFinal published version, 2.68 MBLicence: CC BY

https://urn.fi/URN:NBN:fi:tuni-2025102110025Licence: CC BY

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Chahal, G., Eichenlaub, M. P., Tondl, M., Pawlak, M., Mohenska, M., Grimm, L., Bottrell, L., Drvodelic, M., Alaei, S., Hallab, J., Waylen, L. N., Polo, J. M., Blanpain, C., Palpant, N., Rossello, F. J., Änkö, M. L., Currie, P. D., Hogan, B. M., Winata, C., ... Ramialison, M. (2025). Epigenomics and transcriptomics profiles of developing zebrafish heart cells. Scientific Data, 12, Article 1620. https://doi.org/10.1038/s41597-025-05895-9

@article{113fbe3952d64600a2b9e254af5754ab,

title = "Epigenomics and transcriptomics profiles of developing zebrafish heart cells",

abstract = "cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.",

author = "Gulrez Chahal and Eichenlaub, \{Michael P.\} and Markus Tondl and Micha{\l} Pawlak and Monika Mohenska and Lin Grimm and Lauren Bottrell and Mark Drvodelic and Sara Alaei and Jeannette Hallab and Waylen, \{Lisa N.\} and Polo, \{Jose M.\} and C{\'e}dric Blanpain and Nathan Palpant and Rossello, \{Fernando J.\} and {\"A}nk{\"o}, \{Minna Liisa\} and Currie, \{Peter D.\} and Hogan, \{Benjamin M.\} and Cecilia Winata and Ekaterina Salimova and Nim, \{Hieu T.\} and Mirana Ramialison",

note = "Publisher Copyright: {\textcopyright} Crown 2025.",

year = "2025",

doi = "10.1038/s41597-025-05895-9",

language = "English",

volume = "12",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Research",

}

Chahal, G, Eichenlaub, MP, Tondl, M, Pawlak, M, Mohenska, M, Grimm, L, Bottrell, L, Drvodelic, M, Alaei, S, Hallab, J, Waylen, LN, Polo, JM, Blanpain, C, Palpant, N, Rossello, FJ, Änkö, ML, Currie, PD, Hogan, BM, Winata, C, Salimova, E, Nim, HT & Ramialison, M 2025, 'Epigenomics and transcriptomics profiles of developing zebrafish heart cells', Scientific Data, vol. 12, 1620. https://doi.org/10.1038/s41597-025-05895-9

TY - JOUR

T1 - Epigenomics and transcriptomics profiles of developing zebrafish heart cells

AU - Chahal, Gulrez

AU - Eichenlaub, Michael P.

AU - Tondl, Markus

AU - Pawlak, Michał

AU - Mohenska, Monika

AU - Grimm, Lin

AU - Bottrell, Lauren

AU - Drvodelic, Mark

AU - Alaei, Sara

AU - Hallab, Jeannette

AU - Waylen, Lisa N.

AU - Polo, Jose M.

AU - Blanpain, Cédric

AU - Palpant, Nathan

AU - Rossello, Fernando J.

AU - Änkö, Minna Liisa

AU - Currie, Peter D.

AU - Hogan, Benjamin M.

AU - Winata, Cecilia

AU - Salimova, Ekaterina

AU - Nim, Hieu T.

AU - Ramialison, Mirana

PY - 2025

Y1 - 2025

N2 - cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.

AB - cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.

UR - https://www.scopus.com/pages/publications/105017950071

U2 - 10.1038/s41597-025-05895-9

DO - 10.1038/s41597-025-05895-9

M3 - Data article

C2 - 41057362

AN - SCOPUS:105017950071

SN - 2052-4463

VL - 12

JO - Scientific Data

JF - Scientific Data

M1 - 1620

ER -

Epigenomics and transcriptomics profiles of developing zebrafish heart cells

Abstract

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